Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_038208210.1 Q392_RS13545 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000745855.1:WP_038208210.1 Length = 254 Score = 246 bits (629), Expect = 3e-70 Identities = 133/256 (51%), Positives = 182/256 (71%), Gaps = 3/256 (1%) Query: 1 MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADI 60 M I + +V+G ASGLG ATA+ L GA+V ++D NA+ A E+G A FA DI Sbjct: 1 MKIEGQSALVTGGASGLGEATARELARLGARVAVLDRNAELAAKVAAEIG-GAAFA-CDI 58 Query: 61 SDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQG-PHGLASFAKVINVNLIGSF 119 +D + ++A+ A +A G L+N AGI A++++GK G P L FA+V+NVNLIG++ Sbjct: 59 TDTASVEAALAGAEAAHGPARILMNVAGIGSAKRIVGKDGSPAPLEDFARVVNVNLIGTY 118 Query: 120 NLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAREL 179 N+ RL AA A+ A + GERGV++ TAS+AA+DGQ+GQ AY+ASKG + +TLP AR+L Sbjct: 119 NISRLFAARCAKLDALDGGERGVMMFTASVAAFDGQVGQQAYSASKGGLVGMTLPMARDL 178 Query: 180 ARFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSML 239 A+ GIRV T+APGIF TP++ + + V+ SLAA +PFPPRLG+P E+A LA HI+ N L Sbjct: 179 AQHGIRVCTVAPGIFATPLLLELPEPVQQSLAASIPFPPRLGKPSEFAELACHIVTNGHL 238 Query: 240 NGEVIRLDGALRMAAK 255 NGEVIRLDGALRM+ + Sbjct: 239 NGEVIRLDGALRMSPR 254 Lambda K H 0.318 0.131 0.358 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 198 Number of extensions: 6 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 255 Length of database: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory